N - mixture models by species
modelling N by site to get relative abundance
abundance by site will be used as a cov on predator occupancy
7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ
Species: Â Â Â Â GoldenMantledGroundSquirrel
Detections by Year:
|
Yr
|
2016
|
2017
|
2018
|
2019
|
2020
|
|
sites
|
19
|
31
|
19
|
32
|
26
|
|
detections
|
22
|
55
|
16
|
18
|
29
|
|
N.dot.model
|
10
|
13
|
8
|
7
|
16
|
WAIC
Models by WAIC:
|
model
|
description
|
WAIC
|
N.total.est
|
|
fm7
|
counts
|
21.94854
|
127
|
|
fm6
|
lure + jdt + jdtSq
|
692.44325
|
58
|
|
fm5
|
jdt + jdtSq
|
710.85324
|
50
|
|
fm4
|
lure + jdt
|
731.56568
|
60
|
|
fm2
|
jdt
|
740.01517
|
51
|
|
fm1
|
dot
|
821.73284
|
54
|
|
fm3
|
lure
|
830.35690
|
57
|
Model summaries:
model: fm1
summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
p[1]
|
NA
|
4411
|
0.099
|
0.092
|
0.05
|
0.15
|
0
|
1.001
|
|
p[2]
|
NA
|
8029
|
0.187
|
0.18
|
0.14
|
0.23
|
0
|
1.001
|
|
p[3]
|
NA
|
4186
|
0.047
|
0.044
|
0.02
|
0.08
|
0
|
1.001
|
|
p[4]
|
NA
|
7430
|
0.072
|
0.07
|
0.04
|
0.10
|
0
|
1.001
|
|
p[5]
|
NA
|
4587
|
0.052
|
0.049
|
0.03
|
0.08
|
0
|
1.001
|
|
lambda[1]
|
NA
|
3263
|
0.633
|
0.517
|
0.23
|
0.98
|
0
|
1.001
|
|
lambda[2]
|
NA
|
9003
|
0.418
|
0.361
|
0.21
|
0.62
|
0
|
1.001
|
|
lambda[3]
|
NA
|
3013
|
0.618
|
0.445
|
0.19
|
1.02
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8162
|
0.301
|
0.241
|
0.10
|
0.48
|
0
|
1.001
|
|
lambda[5]
|
NA
|
4666
|
0.836
|
0.682
|
0.41
|
1.24
|
0
|
1.001
|
|
N[110]
|
NA
|
7837
|
0.157
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[78]
|
NA
|
10000
|
0.119
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[54]
|
NA
|
5237
|
0.165
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[40]
|
NA
|
0
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[83]
|
NA
|
9488
|
1.072
|
err
|
1.00
|
1.00
|
err
|
err
|
p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[110]

N[78]

N[54]

N[40]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[83]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
jdt
|
5050
|
1.196
|
1.212
|
0.98
|
1.41
|
0
|
1.001
|
|
alpha0
|
NA
|
4191
|
-2.942
|
-2.935
|
-3.22
|
-2.67
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9140
|
0.576
|
0.518
|
0.27
|
0.87
|
0
|
1.001
|
|
lambda[2]
|
NA
|
9246
|
0.653
|
0.598
|
0.33
|
0.97
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9712
|
0.467
|
0.409
|
0.19
|
0.72
|
0
|
1.001
|
|
lambda[4]
|
NA
|
10000
|
0.258
|
0.22
|
0.10
|
0.41
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9521
|
0.724
|
0.67
|
0.40
|
1.02
|
0
|
1.001
|
|
N[85]
|
NA
|
10000
|
1.028
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[68]
|
NA
|
9627
|
1.086
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[32]
|
NA
|
9295
|
1.422
|
1
|
1.00
|
2.00
|
0
|
1.0001
|
|
N[114]
|
NA
|
10000
|
0.072
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[40]
|
NA
|
10000
|
0.016
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[85]

N[68]

N[32]

N[114]

N[40]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
lure
|
8065
|
-0.093
|
-0.074
|
-0.26
|
0.07
|
0.68622
|
0.8133
|
|
alpha0
|
NA
|
5904
|
-2.449
|
-2.441
|
-2.65
|
-2.23
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9196
|
0.648
|
0.554
|
0.30
|
0.99
|
0
|
1.001
|
|
lambda[2]
|
NA
|
7422
|
0.749
|
0.67
|
0.40
|
1.07
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.411
|
0.326
|
0.16
|
0.63
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9650
|
0.271
|
0.234
|
0.11
|
0.42
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9422
|
0.652
|
0.603
|
0.37
|
0.94
|
0
|
1.001
|
|
N[56]
|
NA
|
10000
|
0.020
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[122]
|
NA
|
10000
|
1.141
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[54]
|
NA
|
10000
|
0.020
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[104]
|
NA
|
9412
|
1.141
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[14]
|
NA
|
10000
|
0.090
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[56]

N[122]

N[54]

N[104]

N[14]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
3620
|
-0.602
|
-0.601
|
-0.83
|
-0.38
|
0
|
1.001
|
|
alpha[2]
|
julianDt
|
3255
|
1.477
|
1.477
|
1.21
|
1.74
|
0
|
1.001
|
|
alpha0
|
NA
|
2557
|
-3.152
|
-3.129
|
-3.47
|
-2.83
|
0
|
1.001
|
|
lambda[1]
|
NA
|
10000
|
0.475
|
0.421
|
0.21
|
0.72
|
0
|
1.001
|
|
lambda[2]
|
NA
|
8912
|
0.523
|
0.457
|
0.25
|
0.78
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.444
|
0.375
|
0.16
|
0.67
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9170
|
0.272
|
0.24
|
0.10
|
0.44
|
0
|
1.001
|
|
lambda[5]
|
NA
|
3270
|
1.353
|
1.173
|
0.62
|
2.02
|
0
|
1.001
|
|
N[88]
|
NA
|
8054
|
0.002
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[44]
|
NA
|
10681
|
0.460
|
0
|
0.00
|
1.00
|
1
|
err
|
|
N[113]
|
NA
|
6728
|
1.547
|
1
|
1.00
|
3.00
|
0
|
1.0001
|
|
N[77]
|
NA
|
10000
|
0.103
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[52]
|
NA
|
10000
|
0.032
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[88]

N[44]

N[113]

N[77]

N[52]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
julianDt
|
1954
|
-0.053
|
-0.054
|
-0.39
|
0.29
|
0.96348
|
0.6068
|
|
alpha[2]
|
julianDtSq
|
1985
|
1.174
|
1.176
|
0.86
|
1.45
|
0
|
1.001
|
|
alpha0
|
NA
|
5409
|
-2.824
|
-2.822
|
-3.08
|
-2.56
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9106
|
0.661
|
0.572
|
0.31
|
1.01
|
0
|
1.001
|
|
lambda[2]
|
NA
|
9606
|
0.466
|
0.402
|
0.22
|
0.70
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9465
|
0.499
|
0.418
|
0.20
|
0.78
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9419
|
0.237
|
0.212
|
0.09
|
0.38
|
0
|
1.001
|
|
lambda[5]
|
NA
|
9358
|
0.734
|
0.653
|
0.41
|
1.05
|
0
|
1.001
|
|
N[39]
|
NA
|
9669
|
0.017
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[63]
|
NA
|
10000
|
1.103
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[93]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[59]
|
NA
|
9608
|
1.272
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[77]
|
NA
|
10000
|
0.001
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[39]

N[63]

N[93]

N[59]

N[77]

julian date relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
3711
|
-0.636
|
-0.619
|
-0.83
|
-0.43
|
0
|
1.001
|
|
alpha[2]
|
julianDt
|
2108
|
0.231
|
0.227
|
-0.13
|
0.57
|
0.6141
|
0.8493
|
|
alpha[3]
|
julianDtSq
|
2326
|
1.216
|
1.23
|
0.92
|
1.53
|
0
|
1.001
|
|
alpha0
|
NA
|
3246
|
-3.123
|
-3.12
|
-3.44
|
-2.80
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9102
|
0.524
|
0.435
|
0.23
|
0.79
|
0
|
1.001
|
|
lambda[2]
|
NA
|
10000
|
0.428
|
0.414
|
0.20
|
0.64
|
0
|
1.001
|
|
lambda[3]
|
NA
|
8902
|
0.479
|
0.406
|
0.20
|
0.75
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9823
|
0.248
|
0.202
|
0.10
|
0.39
|
0
|
1.001
|
|
lambda[5]
|
NA
|
3421
|
1.411
|
1.199
|
0.67
|
2.10
|
0
|
1.001
|
|
N[89]
|
NA
|
10303
|
0.178
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[100]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[24]
|
NA
|
10000
|
0.001
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[93]
|
NA
|
10000
|
0.000
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[38]
|
NA
|
10000
|
0.303
|
0
|
0.00
|
1.00
|
1
|
err
|
alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[89]

N[100]

N[24]

N[93]

N[38]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
counts
|
8541
|
16.781
|
16.592
|
14.61
|
18.87
|
0
|
1.001
|
|
alpha0
|
NA
|
8206
|
-5.162
|
-5.122
|
-5.96
|
-4.38
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9903
|
0.982
|
0.877
|
0.43
|
1.48
|
0
|
1.001
|
|
lambda[2]
|
NA
|
8693
|
0.949
|
0.851
|
0.45
|
1.40
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9152
|
0.959
|
0.855
|
0.37
|
1.48
|
0
|
1.001
|
|
lambda[4]
|
NA
|
6580
|
0.915
|
0.725
|
0.34
|
1.49
|
0
|
1.001
|
|
lambda[5]
|
NA
|
10000
|
0.971
|
0.913
|
0.52
|
1.39
|
0
|
1.001
|
|
N[85]
|
NA
|
7711
|
1.001
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[62]
|
NA
|
10576
|
1.047
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[49]
|
NA
|
9657
|
0.913
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[91]
|
NA
|
9385
|
0.865
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[27]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[85]

N[62]

N[49]

N[91]

N[27]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

alpha relationship
